Two giant petrol tankers capable of carrying more than 100,000 tonnes of fuel between them will be floating at anchor in Melbourne's Port Phillip Bay by Friday afternoon.

Their task is the temporary storage of fuel byproduct from Shell's former Geelong refinery, now owned by Viva Energy.

The timing of the job is uncomfortable for Viva Energy, which has told its only Australian tanker crews that they are no longer needed due to rising road-transported demand in Victoria.

But it also brings into sharp focus simmering concerns among some politicians and groups like the NRMA over Australia's growing reliance on so-called flags of convenience ships to move fuel into and around Australia and the environmental risks those ships pose.

The safety record of some of the 1600 foreign-flagged ships that entered Australian waters in 2013-14 is a major concern for environmentalists who fear a repeat of the 2010 incident when the Chinese bulk carrier Shen Neng 1 slammed into the Great Barrier Reef – or worse.

One of the tankers being loaded in Geelong by Viva Energy on Thursday, was the Kyeema Spirit, a Bahamas-flagged vessel that ran aground near Tallin, Estonia in 2012.

The vessel was warned four times by Estonian authorities for strange navigation before it came to grief.

A spokeswoman for Viva Energy said the Kyeema Spirit's load – and that of the Greek-flagged Sapporo Princess, which will join it in Port Phillip Bay – would be returned to the refinery "shortly" for reprocessing.

Maritime sources said the crews were prepared to be at anchor for up to a month.

Matt Ruchel, the longtime executive director of the Victorian National Parks Association, said ships that are found with more defects – as statistics show foreign-flagged vessels are compared to Australian crewed ships – pose a greater risk to the environment.

The thin mouth of Port Phillip Bay means a spill of oil or refined petrol or diesel product could prove devastating to protected sites like the migratory bird habitats between Werribee and Geelong.

"Port Phillip is an enclosed bay and oil could end up on the shore very quickly. If ships are shoddy it increases the risk of an accident," said Mr Ruchel.

In a speech delivered earlier this month, Deputy Prime Minister Warren Truss said he wanted to reform Labor's Coastal Trading Act which he blames for keeping more foreign ships out of Australian waters.

He called the current system "flawed, bureaucratic and protectionist", saying the liquid fuel industry paid $6.5 million a year per ship due to red tape associated with the act.

Labor argues that its reforms were aimed at arresting the decline in Australian shipping. The number of Australian-flagged vessels carrying interstate cargos has fallen from 55 in 1995 to 23 in 2012. Industry experts say the number will be less than 10 within two years.

Opposition infrastructure spokesman Anthony Albanese said: "If Warren Truss gets his way, we will see more of this WorkChoices on Water happening around the Australian coast, with its adverse impact on Australian skills, shipping reliability, national security and the environment."